TY - JOUR
T1 - Can subtle changes in gene expression be consistently detected with different microarray platforms?
AU - Pedotti, Paola
AU - 't Hoen, Peter A.C.
AU - Vreugdenhil, Erno
AU - Schenk, Geert J.
AU - Vossen, Rolf H.A.M.
AU - Ariyurek, Yavuz
AU - de Hollander, Mattias
AU - Kuiper, Rowan
AU - Van Ommen, Gertjan J.B.
AU - den Dunnen, Johan T.
AU - Boer, Judith M.
AU - de Menezes, Renée X.
N1 - Funding Information:
This work was conducted within the Centre for Medical Systems Biology (CMSB), established by the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research (NGI/NWO). This work has been partially supported by the project BioRange of The Netherlands Bioinformatics Centre (NBIC).
PY - 2008/3/10
Y1 - 2008/3/10
N2 - Background: The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle. Results: Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms. Conclusion: The different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to have higher power for finding differentially expressed genes between groups with small differences in expression.
AB - Background: The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle. Results: Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms. Conclusion: The different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to have higher power for finding differentially expressed genes between groups with small differences in expression.
UR - http://www.scopus.com/inward/record.url?scp=42649121626&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-9-124
DO - 10.1186/1471-2164-9-124
M3 - Article
C2 - 18331641
AN - SCOPUS:42649121626
SN - 1471-2164
VL - 9
JO - BMC Genomics
JF - BMC Genomics
M1 - 124
ER -